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# Install
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Linux operating system. Here tested with Ubuntu 18.04 LTS.
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cutadapt software for dada2 ITS protocol. https://cutadapt.readthedocs.io/en/stable/installation.html
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R version 3.6.1.
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R packages:
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* dada2 https://benjjneb.github.io/dada2/dada-installation.html
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* phyloseq https://bioconductor.org/packages/release/bioc/html/phyloseq.html
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* DECIPHER https://bioconductor.org/packages/release/bioc/html/DECIPHER.html
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* ShortRead http://bioconductor.org/packages/release/bioc/html/ShortRead.html
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* Biostrings http://bioconductor.org/packages/release/bioc/html/Biostrings.html
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* DESeq2 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
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* microbiome https://bioconductor.org/packages/release/bioc/html/microbiome.html
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* metagenomeSeq https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
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* mixOmics https://bioconductor.org/packages/release/bioc/html/mixOmics.html
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* psadd https://github.com/cpauvert/psadd
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* pairwiseAdonis https://github.com/pmartinezarbizu/pairwiseAdonis
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* metacoder https://github.com/grunwaldlab/metacoder
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* nlme https://cran.r-project.org/web/packages/nlme/index.html
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* phangorn https://cran.r-project.org/web/packages/phangorn/index.html
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* plotly https://cran.r-project.org/web/packages/plotly/index.html
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* plyr https://cran.r-project.org/web/packages/plyr/index.html
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* digest https://cran.r-project.org/web/packages/digest/index.html
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* ggpubr https://cran.r-project.org/web/packages/ggpubr/index.html
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* PMCMRplus https://cran.r-project.org/web/packages/PMCMRplus/index.html
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* VennDiagram https://cran.r-project.org/web/packages/VennDiagram/index.html
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* optparse https://cran.r-project.org/web/packages/optparse/index.html
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* futile.logger https://cran.r-project.org/web/packages/futile.logger/index.html
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* devtools https://cran.r-project.org/web/packages/devtools/index.html
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```{R}
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#CRAN packages
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install.packages(c("nlme","phangorn","plotly","plyr","digest","ggpubr","PMCMRplus","VennDiagram","optparse","futile.logger","devtools"))
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#Bioconductor
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if (!requireNamespace("BiocManager", quietly = TRUE))
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install.packages("BiocManager")
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BiocManager::install(c("dada2","phyloseq","DECIPHER","ShortRead","Biostrings","DESeq2","microbiome","metagenomeSeq","mixOmics"))
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#Others
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source("https://bioconductor.org/biocLite.R")
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biocLite("cpauvert/psadd")
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devtools::install_github("pmartinezarbizu/pairwiseAdonis/pairwiseAdonis")
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devtools::install_github("grunwaldlab/metacoder")
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``` |